Literature DB >> 26574307

Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations.

Camilo Velez-Vega1, Daniel J J McKay1, Tom Kurtzman2,3, Vibhas Aravamuthan1, Robert A Pearlstein1, José S Duca1.   

Abstract

A statistical-mechanical framework for estimation of solvation entropies and enthalpies is proposed, which is based on the analysis of water as a mixture of correlated water oxygens and water hydrogens. Entropic contributions of increasing order are cast in terms of a Mutual Information Expansion that is evaluated to pairwise interactions. In turn, the enthalpy is computed directly from a distance-based hydrogen bonding energy algorithm. The resulting expressions are employed for grid-based analyses of Molecular Dynamics simulations. In this first assessment of the methodology, we obtained global estimates of the excess entropy and enthalpy of water that are in good agreement with experiment and examined the method's ability to enable detailed elucidation of solvation thermodynamic structures, which can provide valuable knowledge toward molecular design.

Entities:  

Mesh:

Substances:

Year:  2015        PMID: 26574307      PMCID: PMC4877138          DOI: 10.1021/acs.jctc.5b00439

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  29 in total

1.  Practical Aspects of Free-Energy Calculations: A Review.

Authors:  Niels Hansen; Wilfred F van Gunsteren
Journal:  J Chem Theory Comput       Date:  2014-06-06       Impact factor: 6.006

2.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.

Authors:  Romelia Salomon-Ferrer; Andreas W Götz; Duncan Poole; Scott Le Grand; Ross C Walker
Journal:  J Chem Theory Comput       Date:  2013-08-20       Impact factor: 6.006

3.  Extraction of configurational entropy from molecular simulations via an expansion approximation.

Authors:  Benjamin J Killian; Joslyn Yundenfreund Kravitz; Michael K Gilson
Journal:  J Chem Phys       Date:  2007-07-14       Impact factor: 3.488

4.  Role of the active-site solvent in the thermodynamics of factor Xa ligand binding.

Authors:  Robert Abel; Tom Young; Ramy Farid; Bruce J Berne; Richard A Friesner
Journal:  J Am Chem Soc       Date:  2008-02-12       Impact factor: 15.419

5.  Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril.

Authors:  Crystal N Nguyen; Tom Kurtzman Young; Michael K Gilson
Journal:  J Chem Phys       Date:  2012-07-28       Impact factor: 3.488

6.  Computing the thermodynamic contributions of interfacial water.

Authors:  Zheng Li; Themis Lazaridis
Journal:  Methods Mol Biol       Date:  2012

7.  New hypotheses about the structure-function of proprotein convertase subtilisin/kexin type 9: analysis of the epidermal growth factor-like repeat A docking site using WaterMap.

Authors:  Robert A Pearlstein; Qi-Ying Hu; Jing Zhou; David Yowe; Julian Levell; Bethany Dale; Virendar K Kaushik; Doug Daniels; Susan Hanrahan; Woody Sherman; Robert Abel
Journal:  Proteins       Date:  2010-09

Review 8.  Theory of free energy and entropy in noncovalent binding.

Authors:  Huan-Xiang Zhou; Michael K Gilson
Journal:  Chem Rev       Date:  2009-09       Impact factor: 60.622

9.  Combining solvent thermodynamic profiles with functionality maps of the Hsp90 binding site to predict the displacement of water molecules.

Authors:  Kamran Haider; David J Huggins
Journal:  J Chem Inf Model       Date:  2013-10-15       Impact factor: 4.956

10.  Thermodynamic and Differential Entropy under a Change of Variables.

Authors:  Vladimir Hnizdo; Michael K Gilson
Journal:  Entropy (Basel)       Date:  2010-03-16       Impact factor: 2.524

View more
  8 in total

1.  Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Authors:  Michael E Wall; Gaetano Calabró; Christopher I Bayly; David L Mobley; Gregory L Warren
Journal:  J Am Chem Soc       Date:  2019-03-11       Impact factor: 15.419

2.  Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

Authors:  Steven Ramsey; Crystal Nguyen; Romelia Salomon-Ferrer; Ross C Walker; Michael K Gilson; Tom Kurtzman
Journal:  J Comput Chem       Date:  2016-06-18       Impact factor: 3.376

3.  Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.

Authors:  Lieyang Chen; Anthony Cruz; Daniel R Roe; Andrew C Simmonett; Lauren Wickstrom; Nanjie Deng; Tom Kurtzman
Journal:  J Chem Theory Comput       Date:  2021-04-08       Impact factor: 6.006

4.  On the accuracy of one- and two-particle solvation entropies.

Authors:  Benedict W J Irwin; David J Huggins
Journal:  J Chem Phys       Date:  2017-05-21       Impact factor: 3.488

5.  Comment on "Theoretical studies on a carbonaceous molecular bearing: association thermodynamics and dual-mode rolling dynamics" by H. Isobe, K. Nakamura, S. Hitosugi, S. Sato, H. Tokoyama, H. Yamakado, K. Ohno and H. Kono, Chem. Sci., 2015, 6, 2746.

Authors:  Enrique M Cabaleiro-Lago; Jesús Rodríguez-Otero; Adrià Gil
Journal:  Chem Sci       Date:  2016-02-09       Impact factor: 9.825

6.  Probing the Dynamic Structure-Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory.

Authors:  Hongbin Wan; Vibhas Aravamuthan; Robert A Pearlstein
Journal:  ACS Pharmacol Transl Sci       Date:  2020-11-06

7.  Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets.

Authors:  Crystal N Nguyen; Tom Kurtzman; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2015-12-04       Impact factor: 6.006

8.  Biodynamics: A novel quasi-first principles theory on the fundamental mechanisms of cellular function/dysfunction and the pharmacological modulation thereof.

Authors:  Gianluca Selvaggio; Robert Alan Pearlstein
Journal:  PLoS One       Date:  2018-11-01       Impact factor: 3.240

  8 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.